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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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2
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Rayfield KM, Mychajliw AM, Singleton RR, Sholts SB, Hofman CA. Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health. Proc Biol Sci 2023; 290:20230525. [PMID: 38052246 DOI: 10.1098/rspb.2023.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.
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Affiliation(s)
- Kristen M Rayfield
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexis M Mychajliw
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology & Program in Environmental Studies, Middlebury College, Middlebury, VT 05753-6203, USA
| | - Robin R Singleton
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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3
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Muschick M, Jemmi E, Lengacher N, Hänsch S, Wales N, Kishe MA, Mwaiko S, Dieleman J, Lever MA, Salzburger W, Verschuren D, Seehausen O. Ancient DNA is preserved in fish fossils from tropical lake sediments. Mol Ecol 2023; 32:5913-5931. [PMID: 37830773 DOI: 10.1111/mec.17159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.
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Affiliation(s)
- Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Eliane Jemmi
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Nicholas Lengacher
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Stephanie Hänsch
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Mary A Kishe
- Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Jorunn Dieleman
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | | | - Dirk Verschuren
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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4
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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5
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LeFebvre MJ, Mychajliw AM, Harris GB, Oswald JA. Historical DNA from a rediscovered nineteenth-century paratype reveals genetic continuity of a Bahamian hutia ( Geocapromys ingrahami) population. Biol Lett 2023; 19:20220566. [PMID: 37122196 PMCID: PMC10130705 DOI: 10.1098/rsbl.2022.0566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Past and ongoing human activities have shaped the geographical ranges and diversity of species. New genomic techniques applied to degraded samples, such as those from natural history collections, can uncover the complex evolutionary consequences of human pressures and generate baselines for interpreting magnitudes of species loss or persistence relevant to conservation. Here we integrate mitogenomic data with historical records from a recently rediscovered Bahamian hutia (Geocapromys ingrahami; (FMP Z02816)) specimen at the Fairbanks Museum & Planetarium (Vermont, USA) to determine when and where the specimen was collected and to place it in a phylogenetic context with specimens that both predate (palaeontological) and postdate (archaeological) human arrival in The Bahamas. We determined that this specimen was part of the same population as the named holotype specimen in 1891 on East Plana Cay (EPC). Bahamian hutia populations were widely extirpated following European colonization. Today, EPC hosts the last remaining natural Bahamian hutia population. Mitogenomic data places the focal specimen within the southern Bahamian hutia population, which is now largely restricted to EPC. The results reveal previously undocumented genetic continuity among the EPC population for at least the past 500 years, highlighting how 'dark' museum specimens inform new conservation-relevant understandings of diversity.
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Affiliation(s)
- Michelle J LeFebvre
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Alexis M Mychajliw
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
- Environmental Studies Program, Middlebury College, Middlebury, VT 05753, USA
| | - George B Harris
- Natural History Collections, Fairbanks Museum and Planetarium, St Johnsbury, VT 05819, USA
| | - Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
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6
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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8
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Sanyal A, Larsson J, van Wirdum F, Andrén T, Moros M, Lönn M, Andrén E. Not dead yet: Diatom resting spores can survive in nature for several millennia. AMERICAN JOURNAL OF BOTANY 2022; 109:67-82. [PMID: 34648178 DOI: 10.1002/ajb2.1780] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Understanding the adaptive capacities of species over long timescales lies in examining the revived recent and millennia-old resting spores buried in sediments. We show for the first time the revival, viability, and germination rate of resting spores of the diatom Chaetoceros deposited in sub-seafloor sediments from three ages (recent: 0 to 80 years; ancient: ~1250 (Medieval Climate Anomaly) and ~6600 (Holocene Thermal Maximum) calendar year before present. METHODS Recent and ancient Chaetoceros spores were revived to examine their viability and germination rate. Light and scanning electron microscopy and Sanger sequencing was done to identify the species. RESULTS We show that ~6600 cal. year BP old Chaetoceros resting spores are still viable and that the vegetative reproduction in recent and ancient resting spores varies. The time taken to germinate is three hours to 2 to 3 days in both recent and ancient spores, but the germination rate of the spores decreased with increasing age. The germination rate of the recent spores was ~41% while that of the ancient spores were ~31% and ~12% for the ~1250 and ~6600 cal. year BP old resting spores, respectively. Based on the morphology of the germinated vegetative cells we identified the species as Chaetoceros muelleri var. subsalsum. Sanger sequences of nuclear and chloroplast markers identified the species as Chaetoceros muelleri. CONCLUSIONS We identify a unique model system, Chaetoceros muelleri var. subsalsum and show that recent and ancient resting spores of the species buried in sediments in the Baltic Sea can be revived and used for long-term evolutionary studies.
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Affiliation(s)
- Anushree Sanyal
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
| | - Josefine Larsson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Falkje van Wirdum
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Thomas Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Matthias Moros
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestraße 15, DE-18119 Rostock, Germany
| | - Mikael Lönn
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Elinor Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
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Ovaska U, Bläuer A, Kroløkke C, Kjetså M, Kantanen J, Honkatukia M. The Conservation of Native Domestic Animal Breeds in Nordic Countries: From Genetic Resources to Cultural Heritage and Good Governance. Animals (Basel) 2021; 11:ani11092730. [PMID: 34573696 PMCID: PMC8464703 DOI: 10.3390/ani11092730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Native breeds are domestic animals that have adapted to local conditions. Their genetic and cultural values are high. The conservation of these breeds is maintained by national conservation programmes and agricultural support schemes in Nordic countries. In addition to financial support, the conservation of native breeds requires that their importance in society be widely understood and recognised. This is especially crucial in the local communities in which such breeds are kept. Farmers raising native breeds should be highly motivated to utilise these breeds in animal production. This article examines the extent to which farmers and stakeholders recognise the genetic and cultural significance of conservation, and how the requirements of good governance are met in current conservation arrangements. Moreover, we contemplate the potential to amalgamate the management of animal genetic resources and their cultural environment. Abstract Native breeds are domestic animal populations that have adapted to their habitats. The genetic value of breeds has been known for a long time, and recently more attention has been paid to their cultural value. Due to both ecological and cultural significance, it is important that native breeds continue to be bred in their native environments. This is supported by various financial support schemes. Support schemes rarely cover the financial gap in output compared to commercial breeds. A solution to this has been sought in special products, such as cheese or wool, and other businesses, such as animal-assisted care and tourism. Less attention has been paid to the role of administration and good governance in the maintenance of native breeds. In this study, a questionnaire was sent to all registered keepers of native breeds in Finland. This survey clarified their reasons for keeping native breeds and their ideas for improving governance structures and practices. The results were discussed in stakeholder workshops, and in a Nordic context. The results show that genetic and cultural values are recognised in several documents and programmes, but farmers need to be engaged more in the design of support schemes and practices.
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Affiliation(s)
- Ulla Ovaska
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Auli Bläuer
- School of History, Culture and Arts Studies, University of Turku, 20014 Turku, Finland;
| | - Charlotte Kroløkke
- Department for the Study of Culture, University of Southern Denmark, 5230 Odense, Denmark;
| | - Maria Kjetså
- Nordic Genetic Resource Center, NMBU, P.O. Box 5003, 1432 Ås, Norway;
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600 Jokioinen, Finland;
| | - Mervi Honkatukia
- Nordic Genetic Resource Center, NMBU, P.O. Box 5003, 1432 Ås, Norway;
- Correspondence:
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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12
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Mobilizing the past to shape a better Anthropocene. Nat Ecol Evol 2021; 5:273-284. [PMID: 33462488 DOI: 10.1038/s41559-020-01361-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/08/2020] [Indexed: 01/29/2023]
Abstract
As our planet emerges into a new epoch in which humans dominate the Earth system, it is imperative that societies initiate a new phase of responsible environmental stewardship. Here we argue that information from the past has a valuable role to play in enhancing the sustainability and resilience of our societies. We highlight the ways that past data can be mobilized for a variety of efforts, from supporting conservation to increasing agricultural sustainability and food security. At a practical level, solutions from the past often do not require fossil fuels, can be locally run and managed, and have been tested over the long term. Past failures reveal non-viable solutions and expose vulnerabilities. To more effectively leverage increasing knowledge about the past, we advocate greater cross-disciplinary collaboration, systematic engagement with stakeholders and policymakers, and approaches that bring together the best of the past with the cutting-edge technologies and solutions of tomorrow.
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13
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Amano N, Wang YV, Boivin N, Roberts P. 'Emptying Forests?' Conservation Implications of Past Human-Primate Interactions. Trends Ecol Evol 2021; 36:345-359. [PMID: 33431163 DOI: 10.1016/j.tree.2020.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023]
Abstract
Non-human primates are among the most vulnerable tropical animals to extinction and ~50% of primate species are endangered. Human hunting is considered a major cause of increasingly 'empty forests', yet archaeological data remains under-utilised in testing this assertion over the longer-term. Zooarchaeological datasets allow investigation of human exploitation of primates and the reconstruction of extinction, extirpation, and translocation processes. We evaluate the application and limitations of data from zooarchaeological studies spanning the past 45 000 years in South and Southeast Asia in guiding primate conservation efforts. We highlight that environmental change was the primary threat to many South and Southeast Asian non-human primate populations during much of the Holocene, foreshadowing human-induced land-use and environmental change as major threats of the 21st century.
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Affiliation(s)
- Noel Amano
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Yiming V Wang
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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15
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Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, Orlando L. Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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16
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Quinzin MC, Sandoval-Castillo J, Miller JM, Beheregaray LB, Russello MA, Hunter EA, Gibbs JP, Tapia W, Villalva F, Caccone A. Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:1404-1414. [PMID: 30901116 DOI: 10.1111/cobi.13319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could recapture it. We explored the design elements for establishing a captive-breeding program for Galapagos tortoises (Chelonoidis spp.) built around individuals with admixed ancestry involving an extinct species. The target individuals were hybrids between the extinct species from Floreana Island, C. niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, from Wolf Volcano on Isabela Island. We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward-in-time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Overall genetic diversity was maximized when in the simulation tortoises were organized in relatively small breeding groups. Substantial amounts of the C. niger genome were captured despite limited resources available for selectively breeding tortoises in captivity. Genetic diversity was maximized when captive-bred offspring were released to the wild rather than being used as additional breeders. Our results provide genetic-based and practical guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation.
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Affiliation(s)
- Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Elizabeth A Hunter
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, U.S.A
| | - James P Gibbs
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, 247 Illick Hall, Syracuse, NY, 13210, U.S.A
| | - Washington Tapia
- Giant Tortoise Restoration Initiative, Galapagos Conservancy, Fairfax, VA, 22030, U.S.A
| | - Freddy Villalva
- Galapagos National Park Directorate, Puerto Ayora, Galapagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
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17
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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18
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Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019; 10:E509. [PMID: 31284503 PMCID: PMC6679096 DOI: 10.3390/genes10070509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
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Affiliation(s)
- Tian Ming Lan
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Ren Gui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Hai Meng Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunil Kumar-Sahu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Juan Yang
- Heilongjiang Provincial Museum, Harbin 150001, China
| | - Hua Bing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China
| | - Wen Hao Xu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yan Chun Xu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China.
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19
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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20
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The Promise of Paleogenomics Beyond Our Own Species. Trends Genet 2019; 35:319-329. [PMID: 30954285 DOI: 10.1016/j.tig.2019.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
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21
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Opinion: To curate the molecular past, museums need a carefully considered set of best practices. Proc Natl Acad Sci U S A 2019; 116:1471-1474. [PMID: 30696775 DOI: 10.1073/pnas.1822038116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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22
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Clark DP, Pazdernik NJ, McGehee MR. Polymerase Chain Reaction. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Casas-Marce M, Marmesat E, Soriano L, Martínez-Cruz B, Lucena-Perez M, Nocete F, Rodríguez-Hidalgo A, Canals A, Nadal J, Detry C, Bernáldez-Sánchez E, Fernández-Rodríguez C, Pérez-Ripoll M, Stiller M, Hofreiter M, Rodríguez A, Revilla E, Delibes M, Godoy JA. Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA. Mol Biol Evol 2018; 34:2893-2907. [PMID: 28962023 PMCID: PMC5850336 DOI: 10.1093/molbev/msx222] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.
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Affiliation(s)
- Mireia Casas-Marce
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Begoña Martínez-Cruz
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Maria Lucena-Perez
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Antonio Rodríguez-Hidalgo
- Department of Prehistory, Complutense University, Madrid, Spain.,IDEA (Instituto de Evolución en África), Madrid, Spain.,Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain
| | - Antoni Canals
- Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain.,IPHES, Institut Català de Paleoecologia Humana i Evolució Social (Catalan Institute of Human Paleoecology and Social Evolution), Tarragona, Spain.,Area de Prehistoria (Department of Prehistory), Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleobiología, Instituto Andaluz del Patrimonio Histórico, Consejería de Cultura de la Junta de Andalucía, Seville, Spain
| | | | - Manuel Pérez-Ripoll
- Prehistory and Archaeology Department, University of Valencia, Valencia, Spain
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, Potsdam, Germany
| | - Alejandro Rodríguez
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Eloy Revilla
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Miguel Delibes
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - José A Godoy
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
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24
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Marr MM, Brace S, Schreve DC, Barnes I. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA. Sci Rep 2018; 8:2708. [PMID: 29426903 PMCID: PMC5807398 DOI: 10.1038/s41598-018-21173-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/17/2018] [Indexed: 11/09/2022] Open
Abstract
Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.
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Affiliation(s)
- Melissa M Marr
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
| | - Danielle C Schreve
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
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25
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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26
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West C, Hofman CA, Ebbert S, Martin J, Shirazi S, Dunning S, Maldonado JE. Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2017; 31:1163-1172. [PMID: 27859602 DOI: 10.1111/cobi.12865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/29/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.
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Affiliation(s)
- Catherine West
- Department of Archaeology, Boston University, 675 Commonwealth Avenue, Boston, MA, 02215, U.S.A
| | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, U.S.A
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A
| | - Steve Ebbert
- Alaska Maritime National Wildlife Refuge, U.S. Fish and Wildlife Service, 95 Sterling Hwy #1, Homer, AK, 99603, U.S.A
| | - John Martin
- Alaska Region, U.S. Fish and Wildlife Service, 1011 East Tudor Road, MS 211, Anchorage, AK, 99503, U.S.A
| | - Sabrina Shirazi
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A
| | - Samantha Dunning
- Department of Anthropology, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, U.S.A
| | - Jesus E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, P.O. Box 37012, MRC 5513, Washington, D.C., 20013-7012, U.S.A
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27
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Kistler L, Ware R, Smith O, Collins M, Allaby RG. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res 2017; 45:6310-6320. [PMID: 28486705 PMCID: PMC5499742 DOI: 10.1093/nar/gkx361] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/15/2017] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.
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MESH Headings
- Base Composition
- Base Sequence
- DNA Fragmentation
- DNA, Ancient/analysis
- DNA, Ancient/chemistry
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Deamination
- Genome, Human
- Genome, Mitochondrial
- Humans
- Meta-Analysis as Topic
- Models, Chemical
- Paleontology/methods
- Sequence Analysis, DNA
- Thermodynamics
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Affiliation(s)
- Logan Kistler
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roselyn Ware
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Oliver Smith
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark
| | - Matthew Collins
- Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - Robin G. Allaby
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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28
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Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions. Proc Natl Acad Sci U S A 2017; 113:6388-96. [PMID: 27274046 DOI: 10.1073/pnas.1525200113] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.
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Perry GLW, Wainwright J, Etherington TR, Wilmshurst JM. Experimental Simulation: Using Generative Modeling and Palaeoecological Data to Understand Human-Environment Interactions. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Speller C, van den Hurk Y, Charpentier A, Rodrigues A, Gardeisen A, Wilkens B, McGrath K, Rowsell K, Spindler L, Collins M, Hofreiter M. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150332. [PMID: 27481784 PMCID: PMC4971184 DOI: 10.1098/rstb.2015.0332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2016] [Indexed: 11/30/2022] Open
Abstract
Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Camilla Speller
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Youri van den Hurk
- Institute of Archaeology, University College London, 31-34 Gordon Square, London WC1H 0PY, UK
| | - Anne Charpentier
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE - CNRS, Montpellier Cedex 5, France
| | - Ana Rodrigues
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE - CNRS, Montpellier Cedex 5, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditerranéennes, UMR 5140, CNRS, Labex Archimede IA-ANR-11-LABX-0032-01, Université Paul-Valéry Montpellier, 34970 Lattes, France
| | - Barbara Wilkens
- Dipartimento di Scienze della Natura e del Territorio, Università degli Studi, Sassari, Italy
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Luke Spindler
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, Environment Building, York, North Yorkshire YO10 5DD, UK
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, 14476 Potsdam, Germany
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Waters JM, Grosser S. Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world. Bioessays 2016; 38:1177-1184. [PMID: 27586443 DOI: 10.1002/bies.201600044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts..
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Affiliation(s)
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
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Affiliation(s)
- Alexandre Robert
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - Charles Thévenin
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - Karine Princé
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - François Sarrazin
- UPMC Univ Paris 06 Muséum National d'Histoire Naturelle CNRS CESCO UMR 7204 Sorbonne Universités 75005 Paris France
| | - Joanne Clavel
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
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Lim HC, Braun MJ. High‐throughput
SNP
genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements. Mol Ecol Resour 2016; 16:1204-23. [DOI: 10.1111/1755-0998.12568] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Haw Chuan Lim
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC 20560 USA
| | - Michael J. Braun
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC 20560 USA
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Jones S. Anthropological Archaeology in 2015: Entanglements, Reflection, Reevaluation, and Archaeology beyond Disciplinary Boundaries. AMERICAN ANTHROPOLOGIST 2016. [DOI: 10.1111/aman.12531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sharyn Jones
- Department of Sociology, Anthropology and Philosophy; Northern Kentucky University; Highland Heights KY 41099
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Johnson JA, Altwegg R, Evans DM, Ewen JG, Gordon IJ, Pettorelli N, Young JK. Is there a future for genome-editing technologies in conservation? Anim Conserv 2016. [DOI: 10.1111/acv.12273] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. A. Johnson
- Department of Biological Sciences; Institute of Applied Sciences; University of North Texas; Denton TX USA
| | - R. Altwegg
- Statistics in Ecology, Environment and Conservation; Department of Statistical Sciences, and African Climate and Development Initiative; University of Cape Town; Cape Town South Africa
| | - D. M. Evans
- School of Biology; Newcastle University; Newcastle upon Tyne UK
| | - J. G. Ewen
- Institute of Zoology; Zoological Society of London; London UK
| | - I. J. Gordon
- Division of Tropical Environments and Societies; James Cook University; Townsville Australia
| | - N. Pettorelli
- Institute of Zoology; Zoological Society of London; London UK
| | - J. K. Young
- USDA-NWRC-Predator Research Facility; Department of Wildland Resources; Utah State University; Logan UT USA
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